› 1n5y

X-ray diffraction
3.1Å resolution

HIV-1 Reverse Transcriptase Crosslinked to Post-Translocation AZTMP-Terminated DNA (Complex P)

Released:
DOI: 10.2210/pdb1n5y/pdb
PDB entry 1n5y coloured by chain, front view.
PDB entry 1n5y coloured by chain, side view.
PDB entry 1n5y coloured by chain, top view.
Source organisms:
Primary publication:
Structures of HIV-1 reverse transcriptase with pre- and post-translocation AZTMP-terminated DNA.
Sarafianos SG, Clark AD, Das K, Tuske S, Birktoft JJ, Ilankumaran P, Ramesha AR, Sayer JM, Jerina DM, Boyer PL, Hughes SH, Arnold E
EMBO J 21 6614-24 (2002)
PMID: 12456667

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-114234 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 558 amino acids
Theoretical weight: 64.25 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1157; Coverage: 39%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 430 amino acids
Theoretical weight: 50.28 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1029; Coverage: 30%)
Gene name: gag-pol
Sequence domains:
Structure domains:
Immunoglobulin kappa constant Chain: L
Molecule details ›
Chain: L
Length: 211 amino acids
Theoretical weight: 23.36 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P01837 (Residues: 1-104; Coverage: 97%)
Gene name: Igkc
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Ig gamma-1 chain C region secreted form Chain: H
Molecule details ›
Chain: H
Length: 225 amino acids
Theoretical weight: 24 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P01868 (Residues: 1-102; Coverage: 32%)
Gene names: Igh-4, Ighg1
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
5'-D(*AP*TP*GP*C*TP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3' Chain: T
Molecule details ›
Chain: T
Length: 27 nucleotides
Theoretical weight: 8.37 KDa
5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3' Chain: P
Molecule details ›
Chain: P
Length: 21 nucleotides
Theoretical weight: 6.49 KDa

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
2 modified residues:
Ligand MRG 1 x MRG
Ligand ATM 1 x ATM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P3212
Unit cell:
a: 166.7Å b: 166.7Å c: 221.12Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.255 0.255 0.285
Expression system: Escherichia coli

Quick links

Citations

24 review citations

Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition.
Sarafianos et al. (2009)
23 more

8 mentions without citation

Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review.
Tarasova et al. (2018)
7 more